seq2squiggle/pyproject.toml at main · ZKI-PH-ImageAnalysis/seq2squiggle · GitHub

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[tool.poetry]
name = "seq2squiggle"
version = "0.3.4"
description = "End-to-end simulation of nanopore sequencing signals with feed-forward transformers"
authors = ["Denis Beslic <beslicd@rki.de>"]
license = "MIT"
homepage = "https://github.com/ZKI-PH-ImageAnalysis/seq2squiggle"
repository = "https://github.com/ZKI-PH-ImageAnalysis/seq2squiggle"
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.10"
appdirs = "^1.4.4"
torch = "^2.6.0"
lightning = "^2.2.5"
pod5 = "^0.3.12"
PyGithub = "^2.3.0"
PyYAML = "^6.0.1"
tqdm = "^4.66.2"
numpy = "^1.26.4"
rich-click = "^1.8.2"
wandb = "^0.16.3"
scikit-learn = "^1.4.0"
matplotlib = "^3.9.0"
pysam = "^0.22.0"
prettytable = "^3.9.0"
transformers = "^4.48.0"
numba = "^0.59.0"
pyslow5 = "^1.1.0"
cryptography = "^43.0.3"

[tool.poetry.scripts]
seq2squiggle = "seq2squiggle.seq2squiggle:main"

[tool.coverage.paths]
source = ["src", "*/site-packages"]

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"